Dear George
That is one of the things I would like to implement. I like the idea
very much and it makes sense. You can dress up this with Bayesian
stats and all that, but it is immaterial.
Unfortunately time is always that is not available. I hope in the
nearest future this option will be available in refmac (and may be a
bit more automatic).
There are external restraints option in refmac (now) that should allow
to deal with this problem. If you know distances and angles then it
should be straightforward (but time consuming) to design restraints
manually. Details can be found here:
http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html#External
But I think the question was specifically how to deal with this kind
of cases in SHELXL and SHELXL has sufficient flexibity to deal with
this and other type of cases. This kind of flexibility makes SHELXL
one of the best software available.
with best regards
Garib
On 13 Mar 2009, at 12:35, George M. Sheldrick wrote:
Dear Guenter,
There is a very convenient option in SHELXL for cases like this
where it is reasonable to assume that some distances are equal
but one does not know how long they are: the SADI equal
distance restraint. For an Fe4S4 cluster this might look like:
SADI_FS4 0.02 Fe1 S2 Fe1 S3 Fe1 S4 Fe2 S1 Fe2 S3 Fe2 S4 =
Fe3 S1 Fe3 S2 Fe3 S4 Fe4 S1 Fe4 S2 Fe4 S3
SADI_FS4 0.05 S1 S2 S1 S3 S1 S4 S2 S3 S2 S4 S3 S4
SADI_FS4 0.05 Fe1 Fe2 Fe1 Fe3 Fe1 Fe4 Fe2 Fe3 Fe2 Fe4 Fe3 Fe4
SADI_501 0.02 Fe1 SG_101 Fe2_SG_201 Fe3 SG_301 Fe4 SG_401
SADI_501 0.05 SG_101 S2 SG_101 S3 SG_101 S4 SG_201 S1 SG_201 S3
SG_201 =
S4 SG_301 S1 SG_301 S2 SG_301 S4 SG_401 S1 SG_401 S2 SG_401 S3
I have assumed that there is one FeS4 Cluster (RESI FS4 501) and
that the Cys sulfurs are in residues 101, 201, 301 and 401. To add
more clusters you need to duplicate the last 3 lines with new
residue numbers. At high resolution I would prefer to relax the
esds or refine the cluster without restraints since the oxidation
states of the Fe atoms and hence the distances could differ.
It would be nice to have such restraints in REFMAC too (hint Garib!),
they can be rather useful.
Best wishes, George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Wed, 11 Mar 2009, Guenter Fritz wrote:
Dear All,
I am looking for a set of suitable restraints for 4Fe4S clusters
in shelxl
refinement (the PRODRG server does not like Fe). So far I have put
there
distance restraints. Has somebody experience with angle restraints
for the
4Fe4S clusters? Thanks,
Guenter
***********************************
Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: [email protected]
Tel. Office: +49-(0)7531 88 3205 Tel. Lab : +49-(0)7531 88 3687
Fax: +49-(0)7531 88 2966
